T'Pol and other Vulcans secretly formed a counter-mutiny against Archer to put Forrest back in command of the ship. To assist in returning control of the Enterprise to Captain Forrest, T'Pol tempted Tucker with a sexual encounter so that she could mind meld with him, planting a mental suggestion to sabotage the cloaking device on Enterprise, and then had his memories altered.

When Commander Archer later briefed the senior crew regarding a ship the Tholians had obtained from the future of the prime universe, and his plan to seize it, T'Pol was skeptical and objected to the plan. Forrest overruled her objections and proceeded with the mission. When Forrest ordered Archer to take an assault team aboard the USS Defiant, he pulled T'Pol aside and secretly ordered her to kill Archer during the mission. T'Pol never got a chance to carry out the order. While the assault team was on board the Defiant, the Enterprise was attacked and destroyed by Tholian vessels. (ENT: "In a Mirror, Darkly")

In ultimately omitted material from the final draft script of "In a Mirror, Darkly", T'Pol uttered a brief protest to Forrest placing Archer in command of the assault team which was to board the Defiant though she was ignored by Forrest.

T'Pol subsequently helped Archer and the assault team to power up the Defiant, escape the Tholian base and destroy their ships.

After the Enterprise's escape pods were collected by the Defiant, there was a crew complement of only forty seven, not nearly enough to run a Constitution-class vessel on a long term basis. Furthermore, the ship was not fully operational in that the ship's warp drive was off-line.

In desperate need of her scientific expertise, Archer appointed T'Pol as his second-in-command. He made it perfectly clear to her, however, that he bitterly resented her betraying him to Forrest, and that he would order her execution were it not for the fact that no other officer was qualified to replace her while Defiant was only partially operational. Archer contemptuously dismissed T'Pol's argument that it was her duty to stop him, since his orders to relieve Capt. Forrest were fraudulent. He icily told her that he felt the Vulcans were responsible for the rebellion against the Terran Empire, and gave her dire warnings as to what would happen to her should she betray him a second time.

T'Pol studied the Defiant's historical database and learned of the United Federation of Planets that was eventually formed in its universe. She was intrigued by the fact that it was an alliance of several alien races, all of whom were regarded as equals.

T'Pol became alarmed when Archer killed AdmiralBlack and announced his intention to return to Earth, overthrow the Emperor and take the throne for himself. She feared that many Vulcans would be killed under his reign, as he blamed them for the rebellion. She enlisted the help of Soval, a Vulcan crewman on board the ISS Avenger, and downloaded the Defiant's tactical information to him before Archer had her and all other alien crew members transferred off Defiant to the Avenger.

Both T'Pol and Soval convinced Phlox to sabotage the Defiant so the Avenger could destroy it. Before this was done, however, communications officerHoshi Sato discovered the information T'Pol downloaded from the Defiant and arrested T'Pol on the Avenger after fierce hand-to-hand combat.

Interrogated by Archer in Defiant's briefing room

T'Pol was interrogated by Archer and Sato, but despite their best efforts, they failed to get any information out of her. T'Pol defiantly warned Archer that although it may take centuries, Humanity would ultimately pay for its arrogance. Sato, who hated T'Pol, was adamant that Archer execute her for her treachery immediately. Before the execution could be carried out, however, the Defiant's power systems began to fail and the ship was attacked by the Avenger. (ENT: "In a Mirror, Darkly, Part II")

In the final draft script of "In a Mirror, Darkly", T'Pol was described thus; "Her hair is [...] longer, more Human in appearance. This T’Pol is far more harsh and fiercely logical than the Vulcan we know – she views emotion as a weakness."

It was unclear what happened to T'Pol at the end of the episode. However, it is reasonable to assume that both she and any remaining mutineers were likely executed, if not on Archer's orders, then on the orders of Empress Sato.

T'Pol's prediction to Archer regarding the Terran Empire's downfall proved to be prophetic. By the 24th century in the mirror universe, the Terran Empire was destroyed by the Klingon-Cardassian Alliance, and most Terrans were enslaved.